Oh goodness, I know I am weird but I ADORE northern water snakes. And you are right, they are not venomous, but they can be bitey if you try and catch them (and their defense musk is a million times worse than that of a garter snake YUCK!).
However, an adult northern water snake will definitely eat a duckling. Their preferred prey are fish, frogs, and invertebrates, but will take small birds and mammals if available. And since an adult can get quite large, a duckling would be easy pickings. It could not kill an adult duck, fyi. You have several options, protect the duckling and let the snake go about its way. Kill the snake (and it will likely be replaced shortly). Or, relocate the snake (and it will also likely be replaced). Nature abhors a vacuum, if there is a suitable niche to live in, they will move in.